A leak at the Bosveld Phosphates's plant in Phalaborwa, adjacent to the Kruger National Park in Limpopo, has spilled polluted water into rivers that run into the reserve. The plant, which used to be owned by Sasol, produces phosphoric acid, which is used in fertiliser.

Dr Stefanie Freitag-Ronaldson, general manager of scientific services at Kruger Park, said the polluted water started spilling again on Thursday morning. "There have been high levels of processed water spilling into the Selati River."

Her unit had been testing the water and it tested highly acidic. This was flowing into the Selati and then into the Olifants River. This flows through the Kruger National Park into Mozambique and then the Indian Ocean. Fish have died as a direct result of the spill, but it is difficult to quantify the total environmental impact because it could take a long time for these to show – animals that drink the water could become sick but making direct links was difficult.

Nigel Adams, the director of compliance and monitoring at the water affairs department, said that the matter was sub judice so he could not comment on specifics. He was however aware of the recent spills. "We are monitoring the situation because of the rains." If there had been contamination, his unit could add these to the charges that had already been collected from spills that occurred in December of 2013 and January 2014.

These charges were being presented to the National Prosecuting Authority – which handles cases given to it by water affairs – in the next week, he said. If found guilty, the directors of the company could spend five years in jail. An administrative process was also being followed, where water affairs warned the company that it would lose its water-use licence if it did not fix the problem, he said.

Brian Gibson, a spokesperson for Bosveld Phosphates, said a heavy storm on March 5 had resulted in the overflow of their dam. This lasted until March 9. The company had ensured that water would only flow from that one dam if something went wrong, and nowhere else on their site, "in anticipation of such an extreme weather event". The water in this would have its acidity "reduced through chemical treatment", he said.

The company was monitoring the impact on the Selati and Olifants and this had been "minimal due to the improved quality of the process water and flooding of the rivers", he said. Bosveld would continue to take "all reasonable measures" to treat its water and increase the capacity of its dams, he said.

Similar incidents occurred in late December, when heavy rains led to an impoundment dam at its phosphate plant overflowing. The water – waste from the operations – then spilled into the Selati. At the time, the company said it was fixed within 24 hours. A crack in one of the plant's storm water canals was also found, which had been leaking into the river. The water affairs department said at the time that the pH of the Olifants had dropped below 5, where it normally stayed between 7.5 and 8.5, indicating an increased acidity.

Bosveld Phosphates said in a statement that all of this had been fixed by January 6. Andrew McLaggan, its chief executive, said there was so much water in the rivers that there would be no long-term environmental damage because the polluted water would be diluted.

SANParks, which runs the Kruger National Park, said that "several hundred" fish had been killed by the earlier leaks. Spokesperson Ike Phaahla said the environmental fallout was "extensive and spreading". The park had to switch to using boreholes for its tourist camps to ensure clean water, he said.

The department of water affairs also laid criminal charges against the company for polluting a 15km stretch of the Selati River. The National Water Act allows the department to prosecute any company which interferes with water, because it is the custodian of all water.

Freitag-Ronaldson said the heavier rains meant there was more dilution in the river and dead animals and fish would also be swept further away. This made it more difficult to work out the total damage of the spill. "This is probably why the mine is less concerned this time, because you do not have hundreds of dead fish."

The cumulative impact was a further worry, she said. When spills happened, the impact on the environment built up. At the moment, natural systems could recover from these, but cumulatively their limits would be pressed until they broke. "We are just expecting that the environment will absorb these things. It won't."